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Introduction to respirometr

Source: vignettes/respirometr.Rmd
respirometr.Rmd

Get Started with respirometr

Introduction

The respirometr package provides tools for processing and analyzing respirometry data from LI-COR gas analyzers. It currently supports data from LI-850 and LI-7000 analyzers, making it easier to work with these common instruments in R.

Installation

You can install respirometr from GitHub:

# install.packages("devtools")
devtools::install_github("roaldarbol/respirometr")

Basic Usage

First, load the package:

Reading Data Files

The package provides specialized functions for reading data from different LI-COR analyzers:

# Read data from a LI-850 analyzer
li850_data <- read_licor_li850("path/to/LI850.txt")

# Read data from a LI-7000 analyzer
li7000_data <- read_licor_li7000("path/to/LI7000.txt")

These functions automatically: - Handle the specific file formats of each analyzer - Clean column names for easier use in R - Remove columns with NA values - Convert time to a standardized format

Normalizing Data

The package provides two methods for normalizing drift in measurements:

# Using linear interpolation between means
normalized_data <- normalise_drift_means(
  data = measurements,
  pre = pre_measurement_values,
  post = post_measurement_values
)

# Using linear regression
normalized_data <- normalise_drift_lm(
  data = data,
  data_pre = pre_measurements,
  data_post = post_measurements,
  colname_time = "time",
  colname_measure = "co2d_um_m"
)

Next Steps